DNA in the eukaryotic nucleus is packaged into chromatin. The basic component of chromatin is the nucleosome, comprised of an octamer of the core histones H2A, H2B, H3, and H4 encircled by 146 base pairs of DNA. Nucleosomes, in turn, can be tightly packaged by the linker histone H1, which are then further organized into higher-order structures by additional factors, most of which are not well characterized.
Although the basic building blocks of chromatin are known, the protein factors regulating chromatin structure and function are poorly defined or not yet discovered. Modulation of chromatin structure and composition plays a vital role in a variety of basic cellular processes, such as transcription, DNA repair, replication, and mitosis as well as in large scale events in cells and organisms including, but not limited to development, differentiation, and responses to external stimuli. Defects that disrupt chromatin structure can directly elicit human diseases and cancer. Thus, cataloguing the protein composition of chromatin is desirable in order to facilitate the discovery of novel therapeutic targets to stem the progression of disease states.
Current methods to identify the protein composition, as well as other factors, of chromatin, are inadequate and often inappropriate. For example, genetic analyses in yeast of Drosophila, or depletion studies in mammalian cells have identified factors that associate with or regulate chromatin. However, results obtained from these studies are sometimes indirect and oftentimes misleading and thus must be confirmed using additional techniques.